SYLLABUS
MCDB 3500 – Molecular Biology Spring, 2010
MCDB 3500 defines the molecules in cells, and describes the major molecular
processes that lie behind most biological events (replication of DNA, transcription
and processing of RNA, translation of genetic information into proteins), and
emphasizes the techniques and experiments that lead to this information.
Class hours: 12:00 – 12:50, Monday, Wednesday, Friday in Chem 140. The
lectures are your most specific guide to what is important. Never hesitate to ask
questions to clarify what is said during the lectures.
Lecturer: Michael Stowell, Email: Michael.Stowell@colorado.edu.
Office hours: Wednesday 13:00 – 15:00, or by appointment, in MCDB B231.
Teaching fellow: Michelle Smith, Email: Michelle.K.Smith@Colorado.EDU.
TA: Jonathan Langberg, Email: jonathan.langberg@colorado.edu
TA hours : Monday 16:00 & Thursday 10:00 both in MCDB A350
Clickers: We will use clickers for rapid feedback and to foster interactive learning
in a large classroom setting. It will account for 5% of the final grade (see below).
Please
register
your
clicker
by
January
19th
at
http://www.colorado.edu/its/cuclickers/students/register.html. In order for you to
get your clicker points, you must register your clicker!!
Homework: On-line homework will be due every Friday Morning at 11 AM,
except for the first week and on exam weeks. Homework will count for 10% of the
final grade.
Textbook: Robert F. Weaver, Molecular Biology 4th Edition, McGraw-Hill, 2007
is required. This is a relatively new book; the 1st edition was used for the first time
here in 1999. It is particularly strong on experimental detail. In my opinion, it
might be sensible to share a copy with another student, but it will be a distinct
disadvantage if you don’t have easy continuous access to the text. We will look
at most of this text and it is a reasonable and clear reference to own if you will
continue in the biomedical sciences. In any case, it will give you another view of
the material treated in lecture. The subjects treated in lecture are the materials
you will be tested on, though the particular question may be formulated using
material from the book. Reading the same topics in the book explains the
selection of topics a second time, sometimes in greater depth. Some nice
animations and other helpful material related to the book can be found at
http://www.mhhe.com/weaver4. The 3rd Edition is a reasonable substitute but not
a complete substitute as the texts have organization and informational
differences.
Powerpoint lectures: Before each lecture is given, a copy of the powerpoint
lecture (in pdf format) will be uploaded on the course website. You can
SYLLABUS
MCDB 3500 – Molecular Biology Spring, 2010
download and print out the lecture so that you can follow the lecture by taking
notes on it. They comprise a skeletal record of what happens in the lecture, and
will also free your understanding from dependence on the lecturer’s limited
artistic talent. However, you may find these lectures unintelligible without your
own written notes. Therefore, don’t think of them as a second, independent
“book” you can read but instead as a interactive record of the lecture that you will
create.
Clicker questions and practice exams: For most lectures, 1-3 clicker
questions will be given covering the material of the current or previous lectures.
Answers will be discussed right away. These are intended to make you think
about the material that has just been covered and to give the lecturer an
opportunity to observe whether the class in general understands the covered
material. Clicker usage, but NOT whether you answer right or wrong, is part of
your grade (see below). In addition to clicker questions, before each regular term
exam, a copy of a previous comparable MCDB 3500 exam will be given out for
use as practice and preparation. Finally, the “Solved Problems” at the end of
each Weaver Chapter are often useful.
Review sessions: Before each exam during the regular term, there will be a 60minute review session. These are usually held either during class or at 5-6 PM, a
few days before the exam, but may vary because of room availability. In any
case, they will be announced in lecture and are intended to provide for lastminute clarification of any still-obscure points.
Exams & grading: Your grade in MCDB 3500 is based on your final score
relative to the other students in the class. Your final score (0-100 points) will be
calculated the following way:
Clicker use (5%). This is based entirely on clicker use, NOT on whether you get
the answers right. To get credit for the whole semester, make sure that your
clicker is registered with the class at the beginning of the semester!
Homework (10%). This is based on your performance on the weekly on-line
homework and surveys.
Exams 1-3 (20% each). The 3 regular exams during the term are given in class
time, and cover only the material between the exams (i.e. not cumulative). These
term exams each make up 20% of your score. NO term exam can be dropped
and make up exams will only be given for extenuating circumstances.
Final Exam (25%). The final exam will cover i) the lectures between the third term
exam and the final, as well as ii) the concepts (as opposed to the details) of the
material covered in term exams 1-3.
SYLLABUS
MCDB 3500 – Molecular Biology Spring, 2010
Our advice is: MCDB 3500 (like many other university courses) is complex
enough to reward the student who gives some thought to how to take it. The
most important trick is to keep up. The pace is unrelenting because MCDB 3500
must sometimes move rapidly using only ≈40 lectures to cover the field of
molecular biology, which is a rapidly expanding field due to very intense
research.
To prepare for exams:
1. Make sure you understand all topics covered in lecture, homework and the
clicker questions.
2. Read Weaver – preferably before the lectures - and note well topics where
reading and lecture overlap.
3. Do the practice exams.
4. Read through Weaver’s “Solved Problems”. At this point, you should be ready.
Lectures & Reading – The short notes below are to help you find the text in
Weaver relevant to subjects as they arise in lecture. The order may vary a bit
from that shown and there may be minor changes during the semester. Also,
please look at the learning goals on the course website. They will give you an
idea about what we expect you to be able to do in this course.
Weaver - Molecular Biology, 4th edition.
1st term: Jan. 11 – Feb. 10, 2010
Ch 2, p. 12-30, DNA structure and chemistry.
Ch 4, p. 51-78; Ch 5, p. 84,86,88-91,93-94(top),97-101,104-106, Molecular
cloning.
Ch 3, p. 38–42; Ch 6, p. 126-171; Ch 5, p. 116-119, Bacterial transcription.
Ch 7, p.172-188, 192-200; Ch 8, p. 202-224, Transcriptional regulation in
bacteria/phages.
Exam #1. Wednesday, Feb. 10 (Covers material from Jan 11 to Feb 8).
2nd term: Feb. 11 – Mar 8, 2010
Ch 10, p. 250-261, 266-279, Eukaryotic transcription.
Ch 11, p. 280-318; Ch. 5, p 106-119, General transcription factors in eukaryotes.
Ch 9, p. 241-243, Protein-DNA interactions.
Ch 12, p. 321-357, Eukaryotic transcription activators.
Ch 13, p. 359-397, Chromatin.
Exam #2. Monday, Mar 8 (Covers material from Feb 11 to Mar 6).
3rd term:
SYLLABUS
MCDB 3500 – Molecular Biology Spring, 2010
Mar 10 – Apr 12, 2010:
Ch 20, p. 639-660, DNA replication.
Ch 14, p. 399-442, RNA splicing via spliceosomes, other ways.
Ch 15, p. 444-479, mRNA capping and cleavage/polyadenylation.
Ch 16, p. 480-487, rRNA and tRNA processing.
p. 487-494, Trans-splicing and RNA editing.
Exam #3. Monday, Apr 12 (Covers material from Mar 10 to Apr 9).
4th term:
Apr. 12 – April 30, 2009:
Ch 3, p. 42-46, Introduction to translation.
Ch 19, p. 621-633, Ribosomes, tRNA.
Ch 17, p. 521-555, Translation initiation.
Ch 18, p. 564-606, Coding, elongation, and termination.
Ch 16, p. 494-519; Ch 17, p. 556-562, Post-transcriptional control of gene
expression (Iron response regulation, miRNA/siRNA regulation).
Final Exam – Saturday May 1 - 7:30 PM to 10:00 PM (Covers material from Apr
12 to Apr 30 in depth, as well as the general concepts of the material covered
throughout the semester).
SYLLABUS
MCDB 3500 – Molecular Biology Spring, 2010
Disabilities: If you qualify for accommodations because of a disability, please
submit to me a letter from Disability Services in a timely manner so that your
needs be addressed. Disability Services determines accommodations based on
documented disabilities. Contact: 303-492-8671, Willard 322, and
http://www.Colorado.EDU/disabilityservices
If you have a temporary medical condition or injury, see guidelines at
http://www.colorado.edu/disabilityservices/go.cgi?select=temporary.html
Religious observances: Campus policy regarding religious observances
requires that faculty make every effort to deal reasonably and fairly with all
students who, because of religious obligations, have conflicts with scheduled
exams, assignments or required attendance.
In this class, please let me know within the first week of the class if an exam is
scheduled in conflict with a religious obligation so that your needs can be
addressed.
See full details at http://www.colorado.edu/policies/fac_relig.html
Classroom behavior: Students and faculty each have responsibility for
maintaining an appropriate learning environment. Those who fail to adhere to
such behavioral standards may be subject to discipline. Professional courtesy
and sensitivity are especially important with respect to individuals and topics
dealing with differences of race, culture, religion, politics, sexual orientation,
gender, gender variance, and nationalities. Class rosters are provided to the
instructor with the student's legal name. I will gladly honor your request to
address you by an alternate name or gender pronoun. Please advise me of this
preference early in the semester so that I may make appropriate changes to my
records.
See policies at http://www.colorado.edu/policies/classbehavior.html and at
http://www.colorado.edu/studentaffairs/judicialaffairs/code.html - student_code
Sexual Harassment: The University of Colorado at Boulder policy on
Discrimination and Harassment, the University of Colorado policy on Sexual
Harassment and the University of Colorado policy on Amorous Relationships
apply to all students, staff and faculty. Any student, staff or faculty member who
believes s/he has been the subject of sexual harassment or discrimination or
harassment based upon race, color, national origin, sex, age, disability, creed,
religion, sexual orientation, or veteran status should contact the Office of
Discrimination and Harassment (ODH) at 303-492-2127 or the Office of Judicial
Affairs at 303-492-5550. Information about the ODH, the above referenced
policies and the campus resources available to assist individuals regarding
discrimination or harassment can be obtained at http://www.colorado.edu/odh
Honor code: All students of the University of Colorado at Boulder are
responsible for knowing and adhering to the academic integrity policy of this
institution. Violations of this policy may include: cheating, plagiarism, aid of
SYLLABUS
MCDB 3500 – Molecular Biology Spring, 2010
academic dishonesty, fabrication, lying, bribery, and threatening behavior. All
incidents of academic misconduct shall be reported to the Honor Code Council
(honor@colorado.edu; 303-735-2273). Students who are found to be in violation
of the academic integrity policy will be subject to both academic sanctions from
the faculty member and non-academic sanctions (including but not limited to
university probation, suspension, or expulsion). Other information on the Honor
Code can be found at http://www.colorado.edu/policies/honor.html and at
http://www.colorado.edu/academics/honorcode/